Mercurial > repos > saketkc > chasm_web
changeset 7:af0c2fa5bc76 draft
Uploaded
| author | saketkc |
|---|---|
| date | Wed, 16 Jul 2014 20:29:51 -0400 |
| parents | d88b17f16b14 |
| children | 47ca5fb1b3f7 |
| files | chasm_webservice/chasm_webservice.py chasm_webservice/chasm_webservice.xml chasm_webservice/test-data/chasm_input.txt chasm_webservice/test-data/chasm_output_aminoacids.txt chasm_webservice/test-data/chasm_output_error.txt chasm_webservice/test-data/chasm_output_genes.txt chasm_webservice/test-data/chasm_output_variants.txt chasm_webservice/test-data/ma_nucleotide_output.csv chasm_webservice/test-data/ma_proper_nucleotide.csv chasm_webservice/test-data/ma_proper_protein.csv chasm_webservice/test-data/ma_proper_protein.tsv chasm_webservice/test-data/ma_protein_output.csv chasm_webservice/test-data/polyphen2_full.txt chasm_webservice/test-data/polyphen2_input.txt chasm_webservice/test-data/polyphen2_log.txt chasm_webservice/test-data/polyphen2_short.txt chasm_webservice/test-data/polyphen2_snp.txt |
| diffstat | 17 files changed, 26 insertions(+), 207 deletions(-) [+] |
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--- a/chasm_webservice/chasm_webservice.py Tue Apr 15 13:06:25 2014 -0400 +++ b/chasm_webservice/chasm_webservice.py Wed Jul 16 20:29:51 2014 -0400 @@ -40,7 +40,7 @@ 1: 'Amino_Acid_Level_Analysis.csv', 2: 'Gene_Level_Analysis.csv'} -def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None): +def retry(ExceptionToCheck, tries=40000, delay=3, backoff=2, logger=None): '''Retry calling the decorated function using an exponential backoff. http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/ @@ -150,11 +150,13 @@ else: request = requests.post( __URL__, data=stripped_data, files=dict(foo='bar')) + print request.text job_id = json.loads(request.text)['jobid'] return job_id @retry(requests.exceptions.HTTPError) def zip_exists(self, job_id): + print job_id url = 'http://www.cravat.us/results/%s/%s.zip' % (job_id, job_id) zip_download_request = requests.request('GET', url) if zip_download_request.status_code == 404: @@ -243,6 +245,9 @@ parser.add_argument('--amino_acid_level_analysis_out', dest='amino_acid_level_analysis_out', type=str, required=True,) + parser.add_argument('--codon_level_analysis_out', + dest='codon_level_analysis_out', + type=str, required=True,) parser.add_argument('--error_file', dest='error_file_out', type=str, required=True) parser.add_argument('--snv_box_out', dest='snv_box_out', @@ -266,7 +271,8 @@ 'Variant_Analysis.Result.tsv': args.variant_analysis_out, 'Gene_Level_Analysis.Result.tsv': args.gene_analysis_out, 'SnvGet Feature Description.xls': args.snv_features_out, - 'error.txt': args.error_file_out + 'error.txt': args.error_file_out, + 'Codon_Level_Analysis.Result.tsv': args.codon_level_analysis_out, } url = chasm_web.zip_exists(job_id) download = chasm_web.download_zip(url, job_id)
--- a/chasm_webservice/chasm_webservice.xml Tue Apr 15 13:06:25 2014 -0400 +++ b/chasm_webservice/chasm_webservice.xml Wed Jul 16 20:29:51 2014 -0400 @@ -12,19 +12,21 @@ --gene_analysis_out $gene_analysis_out --variant_analysis_out $variant_analysis_out --amino_acid_level_analysis_out $amino_acid_level_analysis_out + --codon_level_analysis_out $codon_level_analysis_out --error_file $error_file + </command> <inputs> <param format="txt" name="input" type="data" label="Variants File" /> <param name="analysis_type" type="select" label="Choose analysis type" help=" - Cancer driver analysis predicts whether\ - the submitted variants are cancer drivers.\ - Functional effect analysis predicts whether\ - the submitted variants will have any\ - functional effect on their translated proteins.\ - Annotation only provides\ - GeneCard and PubMed information on\ - the genes containing the submitted variants."> + Cancer driver analysis predicts whether\ + the submitted variants are cancer drivers.\ + Functional effect analysis predicts whether\ + the submitted variants will have any\ + functional effect on their translated proteins.\ + Annotation only provides\ + GeneCard and PubMed information on\ + the genes containing the submitted variants."> <option value="driver">Cancer driver analysis</option> <option value="functional">Functional effect analysis</option> <option value="geneannotationonly">Annotation only</option> @@ -54,7 +56,7 @@ <option value="Lung-Adenocarcinoma">Lung-Adenocarcinoma</option> <option value="Lung-Squamous_Cell">Lung-Squamous_Cell</option> <option value="Melanoma">Melanoma</option> - <option value="Other">Other</option> + <option value="Other" selected="true">Other</option> <option value="Ovary">Ovary</option> <option value="Pancreas">Pancreas</option> <option value="Prostate-Adenocarcinoma">Prostate-Adenocarcinoma</option> @@ -70,17 +72,19 @@ <data format="tabular" name="variant_analysis_out" label="${tool.name} on ${on_string}: variant" /> <data format="tabular" name="amino_acid_level_analysis_out" label="${tool.name} on ${on_string}: aminoacid" /> <data format="tabular" name="error_file" label="${tool.name} on ${on_string}: error" /> + <data format="tabular" name="codon_level_analysis_out" label="${tool.name} on ${on_string}: Codon level" /> </outputs> <tests> <test> <param name="input" value="chasm_input.txt"/> - <param name="gene_annotation" value="yes"/> + <param name="gene_annotation" value="no"/> <param name="analysis_type" value="driver"/> <param name="tissue_type" value="Other"/> - <output name="gene_analysis_out" file="chasm_output_genes.txt"/> - <output name="variant_analysis_out" file="chasm_output_variants.txt"/> - <output name="amino_acid_level_analysis_out" file="chasm_output_aminoacids.txt"/> - <output name="error_file" file="chasm_output_error.txt"/> + <output name="gene_analysis_out" file="chasm_output_genes.tabular" lines_diff="4" ftype="tabular"/> + <output name="variant_analysis_out" file="chasm_output_variants.tabular" lines_diff="4"/> + <output name="amino_acid_level_analysis_out" file="chasm_output_aminoacids.tabular"/> + <output name="error_file" file="chasm_output_errors.tabular" lines_diff="4"/> + <output name="codon_level_analysis_out" file="chasm_output_codons.tabular" lines_diff="4"/> </test> </tests>
--- a/chasm_webservice/test-data/chasm_input.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -TR1 chr22 30421786 + A T -TR2 chr22 29446079 + A G -TR3 chr22 29446079 + A G -TR4 chr22 40814500 - A G -TR5 chr22 40815256 + C T
--- a/chasm_webservice/test-data/chasm_output_aminoacids.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#Amino Acid Level Analysis Report -#2014-04-14 18:52:00.963260 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at amino acid level. -#Input coordinate was hg19 genomic. -#For more information on CRAVAT, visit http://www.cravat.us. -# -Transcript Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) HUGO symbol Other transcripts Occurrences in study [amino acid change] Transcript by COSMIC AA change by COSMIC Occurrences in COSMIC [amino acid change] Occurrences in COSMIC by primary sites [amino acid change] -NM_021090.3 1198 MS N I MTMR3 NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 1 0 -NM_001206998.1 637 MS H R ZNRF3 NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 2 0 -NM_020831.3 648 MS S G MKL1 ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 1 ENST00000355630 p.S648G (stomach 1) 1 stomach(1 ) -NM_020831.3 396 MS A T MKL1 ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 1 0
--- a/chasm_webservice/test-data/chasm_output_error.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -# End of input format error output. If nothing is above this line, there was no format error in the input. \ No newline at end of file
--- a/chasm_webservice/test-data/chasm_output_genes.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#Gene Level Analysis Report -#2014-04-14 18:52:00.963904 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at gene level. -#The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance. -#Input coordinate was hg19 genomic. -#Tissue type for CHASM analysis: Other -#For more information on CRAVAT, visit http://www.cravat.us. -# -HUGO symbol Best driver score from representative transcripts Composite p value Composite FDR Occurrences in study [gene mutated] Occurrences in COSMIC [gene mutated] Occurrences in COSMIC by primary sites [gene mutated] -MTMR3 0.6 0.3364 0.55 1 102 upper_aerodigestive_tract(2);large_intestine(24);haematopoietic_and_lymphoid_tissue(5);endometrium(12);urinary_tract(4);oesophagus(1);liver(3);skin(17);lung(17);ovary(5);prostate(2);kidney(4);breast(6 ) -ZNRF3 0.514 0.171 0.55 2 73 upper_aerodigestive_tract(2);large_intestine(19);autonomic_ganglia(1);haematopoietic_and_lymphoid_tissue(2);endometrium(12);urinary_tract(2);lung(16);liver(5);skin(1);oesophagus(3);ovary(2);NS(1);prostate(2);kidney(3);breast(2 ) -MKL1 0.728 0.793956248886469 1 2 68 large_intestine(15);stomach(2);central_nervous_system(1);haematopoietic_and_lymphoid_tissue(3);endometrium(13);urinary_tract(1);lung(19);breast(3);skin(1);ovary(5);kidney(4);liver(1 )
--- a/chasm_webservice/test-data/chasm_output_variants.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -#Variant Level Analysis Report -#2014-04-14 18:52:00.964521 -#Analysis done at http://www.cravat.us. -#Input file: dataset_34.dat -#This report shows analysis results at variant level. -#Input coordinate was hg19 genomic. -#Tissue type for CHASM analysis: Other -#For more information on CRAVAT, visit http://www.cravat.us. -# -ID Chromosome Position Strand Reference base Alternate base Sample ID HUGO symbol Transcript Transcript strand Codon change Amino acid position Sequence Ontology Reference amino acid(s) Alternate amino acid(s) Other transcripts Mappability Warning Driver score of representative transcript (driver mutations close to 0) Empirical p-value FDR (Benjamini-Hochberg) (not available with less than 10 unique mutations) Best driver score and transcript All transcripts and driver scores dbSNP 1000 Genomes allele frequency ESP6500 allele frequency (European American) ESP6500 allele frequency (African American) Occurrences in study [exact nucleotide change] Transcript by COSMIC AA change by COSMIC Occurrences in COSMIC [exact nucleotide change] Occurrences in COSMIC by primary sites [exact nucleotide change] -TR1 CHR22 30421786 + A T No_sample_ID MTMR3 NM_021090.3 + aAc>aTc 1198 MS N I NM_153051.2:aAc>aTc:N1161I, NM_153050.2:aAc>aTc:N1170I, ENST00000323630:aAc>aTc:N1062I, ENST00000351488:aAc>aTc:N1161I, ENST00000333027:aAc>aTc:N1170I, ENST00000406629:aAc>aTc:N1170I, ENST00000401950:aAc>aTc:N1198I 0.6(NM_021090.3:N1198I) 0.3364 0.60 0.572(ENST00000323630:N1062I) ENST00000323630:N1062I(0.572),ENST00000406629:N1170I(0.602),ENST00000401950:N1198I(0.6),ENST00000351488:N1161I(0.572),NM_153050.2:N1170I(0.572),ENST00000333027:N1170I(0.572),NM_021090.3:N1198I(0.6),NM_153051.2:N1161I(0.572) rs75623810 0.00778388278388 0 0.0226963 1 -TR2 CHR22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00569767 0.000907853 2 -TR3 CHR22 29446079 + A G No_sample_ID ZNRF3 NM_001206998.1 + cAc>cGc 637 MS H R NM_032173.3:cAc>cGc:H537R, ENST00000406323:cAc>cGc:H537R, ENST00000332811:cAc>cGc:H537R, ENST00000402174:cAc>cGc:H537R, ENST00000544604:cAc>cGc:H637R 0.514(NM_001206998.1:H637R) 0.1710 0.60 0.442(ENST00000544604:H637R) ENST00000544604:H637R(0.442),NM_032173.3:H537R(0.514),ENST00000402174:H537R(0.514),ENST00000406323:H537R(0.514),NM_001206998.1:H637R(0.514),ENST00000332811:H537R(0.514) rs62641746 0 0.00569767 0.000907853 2 -TR4 CHR22 40814500 - A G No_sample_ID MKL1 NM_020831.3 - Agc>Ggc 648 MS S G ENST00000396617:Agc>Ggc:S648G, ENST00000402042:Agc>Ggc:S598G, ENST00000407029:Agc>Ggc:S648G, ENST00000355630:Agc>Ggc:S648G 0.728(NM_020831.3:S648G) 0.6890 0.80 0.708(ENST00000402042:S598G) ENST00000407029:S648G(0.728),NM_020831.3:S648G(0.728),ENST00000396617:S648G(0.728),ENST00000355630:S648G(0.728),ENST00000402042:S598G(0.708) rs878756 0.419871794872 0.396977 0.860645 1 ENST00000355630 p.S648G (stomach 1) 1 stomach(1) -TR5 CHR22 40815256 + C T No_sample_ID MKL1 NM_020831.3 - Gcc>Acc 396 MS A T ENST00000396617:Gcc>Acc:A396T, ENST00000402042:Gcc>Acc:A346T, ENST00000407029:Gcc>Acc:A396T, ENST00000355630:Gcc>Acc:A396T 0.748(NM_020831.3:A396T) 0.7476 0.80 0.748(ENST00000407029:A396T) ENST00000407029:A396T(0.748),NM_020831.3:A396T(0.748),ENST00000396617:A396T(0.748),ENST00000355630:A396T(0.748),ENST00000402042:A346T(0.754) rs34736200 0.0201465201465 0.00127907 0.0832955 1
--- a/chasm_webservice/test-data/ma_nucleotide_output.csv Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","hg19,13,32912555,G,T","D1355Y","BRCA2","http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y","","low","1.24","BRCA2_HUMAN","NP_000050","14","chr13:32912555","","","","" -"2","hg19,7,55178574,G,A","","","","","","","","","0","","","","","" -"3","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
--- a/chasm_webservice/test-data/ma_proper_nucleotide.csv Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -13,32912555,G,T BRCA2 -7,55178574,G,A GBM -7,55178574,G,A GBM
--- a/chasm_webservice/test-data/ma_proper_protein.csv Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -EGFR_HUMAN,R521K -EGFR_HUMAN,R98Q,Polymorphism -EGFR_HUMAN,G719D,disease -NP_000537,G356A -NP_000537,G360A,dbSNP:rs35993958 -NP_000537,S46A,Abolishes,phosphorylation
--- a/chasm_webservice/test-data/ma_proper_protein.tsv Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -EGFR_HUMAN R521K -EGFR_HUMAN R98Q Polymorphism -EGFR_HUMAN G719D disease -NP_000537 G356A -NP_000537 G360A dbSNP:rs35993958 -NP_000537 S46A Abolishes phosphorylation
--- a/chasm_webservice/test-data/ma_protein_output.csv Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","EGFR_HUMAN R521K","R521K","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=482&re=681&var=R521K","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=482&to=681&var=R521K","neutral","0.405","EGFR_HUMAN","NP_005219","399","chr7:55196748","1","1","","" -"2","EGFR_HUMAN R98Q","R98Q","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=57&re=168&var=R98Q","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=57&to=168&var=R98Q","neutral","0.6","EGFR_HUMAN","NP_005219","181","chr7:55178543","","","","" -"3","EGFR_HUMAN G719D","G719D","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719D","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719D","medium","3.115","EGFR_HUMAN","NP_005219","700","chr7:55209201","1","1","","0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ" -"4","NP_000537 G356A","G356A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=318&re=359&var=G356A","http://getma.org/pdb.php?prot=P53_HUMAN&from=318&to=359&var=G356A","neutral","-0.895","P53_HUMAN","NP_000537","45","chr17:7514684","","1","","" -"5","NP_000537 G360A","G360A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=360&re=393&var=G360A","","medium","2.25","P53_HUMAN","NP_000537","15","chr17:7514672","","","","" -"6","NP_000537 S46A","S46A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=30&re=94&var=S46A","http://getma.org/pdb.php?prot=P53_HUMAN&from=30&to=94&var=S46A","neutral","0.55","P53_HUMAN","NP_000537","5","chr17:7520274","1","1","",""
--- a/chasm_webservice/test-data/polyphen2_full.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 nt1 nt2 prediction based_on effect pph2_class pph2_prob pph2_FPR pph2_TPR pph2_FDR site region PHAT dScore Score1 Score2 MSAv Nobs Nstruct Nfilt PDB_id PDB_pos PDB_ch ident length NormASA SecStr MapReg dVol dProp B-fact H-bonds AveNHet MinDHet AveNInt MinDInt AveNSit MinDSit Transv CodPos CpG MinDJxn PfamHit IdPmax IdPSNP IdQmin -Q13615-2 1170 N I ? Q13615-2 1170 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +2.214 -1.705 -3.919 2 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -2313 ? 1.268 ? 47.09 # chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690 -Q13615 1198 N I ? Q13615 1198 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 NO NO ? +2.296 -1.580 -3.876 2 38 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -3099 NO 1.010 ? 45.58 # chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576 -Q13615-3 1161 N I ? Q13615-3 1161 N I A T probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +2.214 -1.705 -3.919 2 37 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0 -3099 ? 1.275 ? 47.37 # chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691 -Q9ULT6 637 H R ? Q9ULT6 637 H R A G benign alignment ? neutral 0.002 0.704 0.987 0.452 NO NO ? +0.398 -2.258 -2.656 2 47 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 2 +858 NO 20.363 20.363 77.46 # chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549 -Q9ULT6 637 H R ? Q9ULT6 637 H R A G benign alignment ? neutral 0.002 0.704 0.987 0.452 NO NO ? +0.398 -2.258 -2.656 2 47 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 2 -1599 NO 20.363 20.363 77.46 # chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549 -Q969V6 648 S C ? Q969V6 648 S C A T possibly damaging alignment ? deleterious 0.89 0.0639 0.821 0.0953 NO COMPBIAS ? +2.837 -1.909 -4.746 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.320 ? 90.33 # chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R A C benign alignment ? neutral 0.167 0.131 0.92 0.162 NO COMPBIAS ? +1.814 -1.909 -3.723 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.525 ? 90.33 # chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S C ? Q969V6 648 S C A T possibly damaging alignment ? deleterious 0.89 0.0639 0.821 0.0953 NO COMPBIAS ? +2.837 -1.909 -4.746 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.320 ? 90.33 # chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R A C benign alignment ? neutral 0.167 0.131 0.92 0.162 NO COMPBIAS ? +1.814 -1.909 -3.723 2 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.525 ? 90.33 # chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882 -E7ER32 648 S C ? E7ER32 648 S C A T possibly damaging alignment ? deleterious 0.953 0.0514 0.788 0.0812 NO NO ? +2.837 -1.909 -4.746 2 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.255 ? 87.22 # chr22:40814500|TA|uc010gye.1-|MKL1| -E7ER32 648 S R ? E7ER32 648 S R A C benign alignment ? neutral 0.337 0.111 0.901 0.142 NO NO ? +1.814 -1.909 -3.723 2 33 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 2.402 ? 87.22 # chr22:40814500|TG|uc010gye.1-|MKL1| -B0QY83 598 S C ? B0QY83 598 S C A T possibly damaging alignment_mz ? deleterious 0.726 0.0797 0.856 0.112 NO NO ? +2.847 -1.931 -4.778 3 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 0 +123 NO 1.615 ? 91.49 # chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882 -B0QY83 598 S R ? B0QY83 598 S R A C benign alignment_mz ? neutral 0.047 0.168 0.942 0.195 NO NO ? +1.674 -1.931 -3.605 3 31 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 0 2 +123 NO 5.560 ? 91.49 # chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.659 21.659 88.08 # chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.659 21.659 88.08 # chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882 -E7ER32 396 A T ? E7ER32 396 A T G A benign alignment ? neutral 0.009 0.233 0.961 0.247 NO NO ? +0.097 -1.540 -1.637 2 39 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 20.554 20.554 83.58 # chr22:40815256|CT|uc010gye.1-|MKL1| -B0QY83 346 A T ? B0QY83 346 A T G A benign alignment_mz ? neutral 0.008 0.239 0.963 0.252 NO NO ? +0.456 -1.547 -2.003 3 32 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 0 1 +879 NO 21.940 21.940 89.22 # chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882 -## Sources: -## Predictions: PolyPhen-2 v2.2.2r398 -## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) -## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) -## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- a/chasm_webservice/test-data/polyphen2_input.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -chr22:30421786 A/T -chr22:29446079 A/G -chr22:40814500 A/G -chr22:40815256 C/T -
--- a/chasm_webservice/test-data/polyphen2_log.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -=========================== -Stage 1/7: Validating input -=========================== -No errors - -=============================== -Stage 2/7: Mapping genomic SNPs -=============================== -WARNING: (chr22:40814500 - uc003ayv.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc003ayw.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc010gye.1) None of the input alleles (A/G) matches reference allele (T) -WARNING: (chr22:40814500 - uc010gyf.1) None of the input alleles (A/G) matches reference allele (T) -Total errors/warnings: 4 - -============================ -Stage 3/7: Collecting output -============================ -No errors - -=============================================== -Stage 4/7: Building MSA and annotating proteins -=============================================== -No errors - -============================ -Stage 5/7: Collecting output -============================ -No errors - -===================== -Stage 6/7: Predicting -===================== -No errors - -============================= -Stage 7/7: Generating reports -============================= -No errors
--- a/chasm_webservice/test-data/polyphen2_short.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 prediction pph2_prob pph2_FPR pph2_TPR -Q13615-2 1170 N I ? Q13615-2 1170 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agu.3+|MTMR3|NP_694690 -Q13615 1198 N I ? Q13615 1198 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agv.3+|MTMR3|NP_066576 -Q13615-3 1161 N I ? Q13615-3 1161 N I probably damaging 0.998 0.0112 0.273 # chr22:30421786|AT|uc003agw.3+|MTMR3|NP_694691 -Q9ULT6 637 H R ? Q9ULT6 637 H R benign 0.002 0.704 0.987 # chr22:29446079|AG|uc003aeg.2+|ZNRF3|NP_115549 -Q9ULT6 637 H R ? Q9ULT6 637 H R benign 0.002 0.704 0.987 # chr22:29446079|AG|uc003aeh.1+|ZNRF3|NP_115549 -Q969V6 648 S C ? Q969V6 648 S C possibly damaging 0.89 0.0639 0.821 # chr22:40814500|TA|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R benign 0.167 0.131 0.92 # chr22:40814500|TG|uc003ayv.1-|MKL1|NP_065882 -Q969V6 648 S C ? Q969V6 648 S C possibly damaging 0.89 0.0639 0.821 # chr22:40814500|TA|uc003ayw.1-|MKL1|NP_065882 -Q969V6 648 S R ? Q969V6 648 S R benign 0.167 0.131 0.92 # chr22:40814500|TG|uc003ayw.1-|MKL1|NP_065882 -E7ER32 648 S C ? E7ER32 648 S C possibly damaging 0.953 0.0514 0.788 # chr22:40814500|TA|uc010gye.1-|MKL1| -E7ER32 648 S R ? E7ER32 648 S R benign 0.337 0.111 0.901 # chr22:40814500|TG|uc010gye.1-|MKL1| -B0QY83 598 S C ? B0QY83 598 S C possibly damaging 0.726 0.0797 0.856 # chr22:40814500|TA|uc010gyf.1-|MKL1|NP_065882 -B0QY83 598 S R ? B0QY83 598 S R benign 0.047 0.168 0.942 # chr22:40814500|TG|uc010gyf.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc003ayv.1-|MKL1|NP_065882 -Q969V6 396 A T ? Q969V6 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc003ayw.1-|MKL1|NP_065882 -E7ER32 396 A T ? E7ER32 396 A T benign 0.009 0.233 0.961 # chr22:40815256|CT|uc010gye.1-|MKL1| -B0QY83 346 A T ? B0QY83 346 A T benign 0.008 0.239 0.963 # chr22:40815256|CT|uc010gyf.1-|MKL1|NP_065882 -## Sources: -## Predictions: PolyPhen-2 v2.2.2r398 -## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) -## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) -## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- a/chasm_webservice/test-data/polyphen2_snp.txt Tue Apr 15 13:06:25 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#snp_pos str gene transcript ccid ccds cciden refa type ntpos nt1 nt2 flanks trv cpg jxdon jxacc exon cexon jxc dgn cdnpos frame cdn1 cdn2 aa1 aa2 aapos spmap spacc spname refs_acc dbrsid dbobsrvd dbavHet dbavHetSE dbRmPaPt comments -chr22:30421786 + MTMR3 uc003agu.3 ? CCDS13871.1 1 A/T missense 142629 A T AC 1 0 -2313 -168 20/20 18/18 ? 0 1170 1 AAC ATC N I 1170 1 Q13615-2 MTMR3_HUMAN NP_694690 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:30421786 + MTMR3 uc003agv.3 16552 CCDS13870.1 1 A/T missense 142629 A T AC 1 0 -3099 -168 20/20 18/18 ? 0 1198 1 AAC ATC N I 1198 1 Q13615 MTMR3_HUMAN NP_066576 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:30421786 + MTMR3 uc003agw.3 ? CCDS46682.1 1 A/T missense 142629 A T AC 1 0 -3099 -168 19/19 17/17 ? 0 1161 1 AAC ATC N I 1161 1 Q13615-3 MTMR3_HUMAN NP_694691 rs75623810 A/T 0.016564 0.089485 A>A>A -chr22:29446079 + ZNRF3 uc003aeg.2 16531 CCDS42999.1 1 A/G missense 166190 A G CC 0 2 +858 -895 8/9 7/8 ? 0 537 1 CAC CGC H R 637 1 Q9ULT6 ZNRF3_HUMAN NP_115549 rs62641746 A/G 0.030762 0.120144 A>A>A -chr22:29446079 + ZNRF3 uc003aeh.1 ? CCDS42999.1 0.982 A/G missense 63040 A G CC 0 2 -1599 -895 7/7 7/7 ? 0 537 1 CAC CGC H R 637 1 Q9ULT6 ZNRF3_HUMAN NP_115549 rs62641746 A/G 0.030762 0.120144 A>A>A -chr22:40814500 - MKL1 uc003ayv.1 ? CCDS14003.1 1 T/A missense 44939 A T CG 1 0 +123 -889 9/12 9/12 ? 0 648 0 AGC TGC S C 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayv.1 ? CCDS14003.1 1 T/G missense 44939 A C CG 1 2 +123 -889 9/12 9/12 ? 0 648 0 AGC CGC S R 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 T/A missense 218191 A T CG 1 0 +123 -889 12/15 9/12 ? 0 648 0 AGC TGC S C 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 T/G missense 218191 A C CG 1 2 +123 -889 12/15 9/12 ? 0 648 0 AGC CGC S R 648 1 Q969V6 MKL1_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc010gye.1 ? ? ? T/A missense 218191 A T CG 1 0 +123 -889 12/15 9/12 ? 0 648 0 AGC TGC S C 648 1 E7ER32 E7ER32_HUMAN ? ? ? ? ? ? -chr22:40814500 - MKL1 uc010gye.1 ? ? ? T/G missense 218191 A C CG 1 2 +123 -889 12/15 9/12 ? 0 648 0 AGC CGC S R 648 1 E7ER32 E7ER32_HUMAN ? ? ? ? ? ? -chr22:40814500 - MKL1 uc010gyf.1 ? ? ? T/A missense 218191 A T CG 1 0 +123 -889 11/14 8/11 ? 0 598 0 AGC TGC S C 598 1 B0QY83 B0QY83_HUMAN NP_065882 ? ? ? ? ? -chr22:40814500 - MKL1 uc010gyf.1 ? ? ? T/G missense 218191 A C CG 1 2 +123 -889 11/14 8/11 ? 0 598 0 AGC CGC S R 598 1 B0QY83 B0QY83_HUMAN NP_065882 ? ? ? ? ? -chr22:40815256 - MKL1 uc003ayv.1 ? CCDS14003.1 1 C/T missense 44183 G A CC 0 1 +879 -133 9/12 9/12 ? 0 396 0 GCC ACC A T 396 1 Q969V6 MKL1_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc003ayw.1 16752 CCDS14003.1 1 C/T missense 217435 G A CC 0 1 +879 -133 12/15 9/12 ? 0 396 0 GCC ACC A T 396 1 Q969V6 MKL1_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc010gye.1 ? ? ? C/T missense 217435 G A CC 0 1 +879 -133 12/15 9/12 ? 0 396 0 GCC ACC A T 396 1 E7ER32 E7ER32_HUMAN ? rs34736200 G/A 0.047299 0.14633 A>A>A -chr22:40815256 - MKL1 uc010gyf.1 ? ? ? C/T missense 217435 G A CC 0 1 +879 -133 11/14 8/11 ? 0 346 0 GCC ACC A T 346 1 B0QY83 B0QY83_HUMAN NP_065882 rs34736200 G/A 0.047299 0.14633 A>A>A -## Totals: -## lines input 4 -## lines skipped 0 -## alleles annotated 17 -## missense 17 -## nonsense 0 -## coding-synon 0 -## intron 0 -## utr-3 0 -## utr-5 0